id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17874 alphafold pae: KeyError: 'pae is not a file in the archive' o.bozkurt@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.10rc202505300032 (2025-05-30 00:32:35 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.10rc202505300032 (2025-05-30) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/obozkurt/Downloads/X/predictions/X/X_model_0.cif Summary of feedback from opening /Users/obozkurt/Downloads/X/predictions/X/X_model_0.cif --- warning | Atom C50 is not in the residue template for LIG /C:1 X_model_0.cif title: . [more info...] Chain information for X_model_0.cif #1 --- Chain | Description A | . B | . Non-standard residues in X_model_0.cif #1 --- LIG — (LIG) No chain in structure corresponds to chain ID given in local score info (chain 'C') Computing secondary structure > open https://www.rbvi.ucsf.edu/chimerax/tutorials.html Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html > alphafold fetch Q86V81 pae true Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json Fetching compressed AlphaFold Q86V81 from https://alphafold.ebi.ac.uk/files/AF-Q86V81-F1-model_v3.cif Chain information for AlphaFold Q86V81 #2 --- Chain | Description | UniProt A | THO complex subunit 4 | THOC4_HUMAN 1-257 Color AlphaFold Q86V81 by residue attribute pLDDT_score Fetching compressed AlphaFold PAE Q86V81 from https://alphafold.ebi.ac.uk/files/AF-Q86V81-F1-predicted_aligned_error_v3.json > close #2 > import json Unknown command: import json > from google.colab import files Unknown command: from google.colab import files > with open('/content/results/ranking_summary.json') as f: Unknown command: with open('/content/results/ranking_summary.json') as f: > data = json.load(f) Unknown command: data = json.load(f) > attr_path = '/content/confidence_scores.attr' Unknown command: attr_path = '/content/confidence_scores.attr' > with open(attr_path, 'w') as f: Unknown command: with open(attr_path, 'w') as f: > f.write(""attribute: confidence_score\n"") Unknown command: f.write(""attribute: confidence_score\n"") > f.write(""recipient: model\n\n"") Unknown command: f.write(""recipient: model\n\n"") > force i, (pose_name, pose_data) in enumerate(data.items(), start=1): force is provided by the uninstalled bundle SEQCROW versions 1.8.19 – 1.8.21 > score = pose_data.get('confidence', 0.0) Unknown command: score = pose_data.get('confidence', 0.0) > f.write(f""{i} {score:.4f}\n"") Unknown command: f.write(f""{i} {score:.4f}\n"") > print(f""✅ Done! Attr file saved to: {attr_path}"") Unknown command: print(f""✅ Done! Attr file saved to: {attr_path}"") > files.download(attr_path) Unknown command: files.download(attr_path) > cartoon style protein thickness 3.4 width 3.4 > color bychain > cartoon style protein thickness 2 width 2 > graphics silhouettes true > lighting soft > cartoon style protein thickness 1 width 2 > 1 Unknown command: 1 > cartoon style protein thickness 3.4 width 3.4 > cartoon style protein thickness 1 width 3.4 > cartoon style protein thickness 1 width 1 > ui tool show ""AlphaFold Error Plot"" > close > open /Users/obozkurt/Desktop/boltz_INF-ERG3_1/INF-ERG3_model_0.cif Summary of feedback from opening /Users/obozkurt/Desktop/boltz_INF-ERG3_1/INF- ERG3_model_0.cif --- warning | Atom C54 is not in the residue template for LIG /C:1 INF-ERG3_model_0.cif title: . [more info...] Chain information for INF-ERG3_model_0.cif #1 --- Chain | Description A | . B | . Non-standard residues in INF-ERG3_model_0.cif #1 --- LIG — (LIG) No chain in structure corresponds to chain ID given in local score info (chain 'C') Computing secondary structure > alphafold pae #1 file /Users/obozkurt/Desktop/boltz_INF-ERG3_1/pae_INF- > ERG3_model_0.npz > color bfactor #1 palette alphafold 6936 atoms, 884 residues, atom bfactor range 31 to 98.3 > color bychain > cartoon style protein thickness 1 width 1 > lighting soft > graphics silhouettes false > graphics silhouettes true > alphafold contacts /a toAtoms /b distance 4 Found 63 residue or atom pairs within distance 4 > select /B:1-785 6191 atoms, 6321 bonds, 785 residues, 1 model selected > select /A:1-98 715 atoms, 724 bonds, 98 residues, 1 model selected > show sel surfaces > select clear > close > open /Users/obozkurt/Desktop/boltz_INF-ERG3/INF-ERG3_model_0.cif Summary of feedback from opening /Users/obozkurt/Desktop/boltz_INF-ERG3/INF- ERG3_model_0.cif --- warnings | Atom C54 is not in the residue template for LIG /B:1 Atom C54 is not in the residue template for LIG /C:1 Atom C54 is not in the residue template for LIG /D:1 INF-ERG3_model_0.cif title: . [more info...] Chain information for INF-ERG3_model_0.cif #1 --- Chain | Description A | . Non-standard residues in INF-ERG3_model_0.cif #1 --- LIG — (LIG) No chain in structure corresponds to chain ID given in local score info (chain 'B') Computing secondary structure > close > open /Users/obozkurt/Desktop/boltz_INF-lipid_1/INF-lipid_model_0.cif Summary of feedback from opening /Users/obozkurt/Desktop/boltz_INF- lipid_1/INF-lipid_model_0.cif --- warning | Atom C54 is not in the residue template for LIG /B:1 INF-lipid_model_0.cif title: . [more info...] Chain information for INF-lipid_model_0.cif #1 --- Chain | Description A | . Non-standard residues in INF-lipid_model_0.cif #1 --- LIG — (LIG) No chain in structure corresponds to chain ID given in local score info (chain 'B') Computing secondary structure > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file /Users/obozkurt/Desktop/boltz_INF-lipid_1/pae_INF- > lipid_model_0.npz > color bfactor #1 palette alphafold 745 atoms, 99 residues, atom bfactor range 55.9 to 97.6 > show surfaces > hide surfaces > Movie record Unknown command: Movie record > movie record > roll y 2 180 > show surfaces > roll x 2 180 > hide surfaces > show surfaces > color #fffffff4 > color #fffffff3 [Repeated 1 time(s)] > color #fffffff2 > color #ffffffe9 > color #ffffffdf > color #ffffffde [Repeated 1 time(s)] > color #ffffffd6 > color #ffffffd3 > color #ffffffce > color #ffffffcd [Repeated 2 time(s)] > color #ffffffce > color #ffffffe2 > color #ffffffe3 > color #ffffffea > color #fffffffb > color #ffffffff > color #7d90ffff > color #90a0ffff > color #90a0fffe > color #90a0fffb > color #90a0ffe6 > color #90a0ffd5 > color #90a0ffd3 > color #90a0ffcb > color #90a0ffc3 > color #90a0ffb8 > color #90a0ffb4 > color #90a0ffb3 [Repeated 1 time(s)] > color #90a0ffb2 > color #90a0ffb1 > color #90a0ffaf > color #90a0ffad > color #90a0ffa3 > color #90a0ffa0 > color #90a0ff9f > color #90a0ff9c > color #90a0ff9b > color #90a0ff9a > color #90a0ff93 > color #90a0ff8e > color #90a0ff8d [Repeated 1 time(s)] > color #90a0ff8c > color #90a0ff8b > color #90a0ff89 > color #90a0ff86 > color #90a0ff77 > color #90a0ff75 > color #90a0ff6a > color #90a0ff69 > color #90a0ff63 > color #90a0ff61 > color #90a0ff60 > color #90a0ff59 > color #90a0ff58 > color #90a0ff57 > color #90a0ff56 > color #90a0ff55 [Repeated 1 time(s)] > color #90a0ff54 > color #90a0ff50 > color #90a0ff4f [Repeated 1 time(s)] > color #90a0ff4e > color #90a0ff4d [Repeated 1 time(s)] > color #90a0ff4c > color #90a0ff4b [Repeated 1 time(s)] > color #90a0ff4a > color #90a0ff48 [Repeated 1 time(s)] > color #90a0ff47 > color #90a0ff46 [Repeated 1 time(s)] > color #90a0ff44 > color #90a0ff37 > color #90a0ff30 [Repeated 1 time(s)] > color #90a0ff2f > color #90a0ff31 > color #90a0ff5f > color #90a0ff62 > color #90a0ff64 > color #90a0ff66 > color #90a0ff69 > color #90a0ff6a > color #90a0ff6f [Repeated 1 time(s)] > color #90a0ff72 > color #90a0ff78 > color #90a0ff7e > color #90a0ff85 > color #90a0ff8c > color #90a0ffeb > color #90a0ffff > movie stop > movie encode output mymovie.mp4 Movie saved to mymovie.mp4 > hide surfaces > color bfactor #1 palette alphafold 745 atoms, 99 residues, 1 surfaces, atom bfactor range 55.9 to 97.6 > alphafold pae #1 colorDomains true > color bychain > movie record > rock y > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file /Users/obozkurt/Desktop/boltz_INF-lipid_1/pae_INF- > lipid_model_0.npz > color bfactor #1 palette alphafold 745 atoms, 99 residues, 1 surfaces, atom bfactor range 55.9 to 97.6 > select /A:1-98 715 atoms, 724 bonds, 98 residues, 1 model selected > show sel surfaces > select clear > stop > hide surfaces > select /A:1-98 715 atoms, 724 bonds, 98 residues, 1 model selected > ui tool show Contacts > contacts sel restrict cross distanceOnly 3.4999999999999996 interModel false > intraMol false select true color #0c0d0c radius 0.085 reveal true 10 distances > rock y > select clear > movie stop > stop > movie encode output mymovie.mp4 Movie saved to mymovie.mp4 > hide #1.2 models > hide #1.1 models > hide #!1 models > show #!1 models > color bychain > movie record > roll y 2 180 > show #1.1 models > select add #1.1 715 atoms, 98 residues, 1 model selected > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file /Users/obozkurt/Desktop/boltz_INF-lipid_1/pae_INF- > lipid_model_0.npz > color bfactor #1 palette alphafold 745 atoms, 99 residues, 1 surfaces, atom bfactor range 55.9 to 97.6 > roll y 2 180 > show #1.2 models > select clear > select /A:1-98 715 atoms, 724 bonds, 98 residues, 1 model selected > show sel surfaces > roll x 2 180 > movie encode output mymovie.mp4 Movie saved to mymovie.mp4 > open > /Users/obozkurt/Desktop/boltz_INF2B_NtREL1B_Bsis_1/INF2B_NtREL1B_Bsis_model_0.cif Summary of feedback from opening /Users/obozkurt/Desktop/boltz_INF2B_NtREL1B_Bsis_1/INF2B_NtREL1B_Bsis_model_0.cif --- warning | Atom C48 is not in the residue template for LIG /C:1 INF2B_NtREL1B_Bsis_model_0.cif title: . [more info...] Chain information for INF2B_NtREL1B_Bsis_model_0.cif #2 --- Chain | Description A | . B | . Non-standard residues in INF2B_NtREL1B_Bsis_model_0.cif #2 --- LIG — (LIG) No chain in structure corresponds to chain ID given in local score info (chain 'C') Computing secondary structure > close > open > /Users/obozkurt/Desktop/boltz_INF2B_NtREL1B_Bsis_1/INF2B_NtREL1B_Bsis_model_0.cif Summary of feedback from opening /Users/obozkurt/Desktop/boltz_INF2B_NtREL1B_Bsis_1/INF2B_NtREL1B_Bsis_model_0.cif --- warning | Atom C48 is not in the residue template for LIG /C:1 INF2B_NtREL1B_Bsis_model_0.cif title: . [more info...] Chain information for INF2B_NtREL1B_Bsis_model_0.cif #1 --- Chain | Description A | . B | . Non-standard residues in INF2B_NtREL1B_Bsis_model_0.cif #1 --- LIG — (LIG) No chain in structure corresponds to chain ID given in local score info (chain 'C') Computing secondary structure > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file > /Users/obozkurt/Desktop/boltz_INF2B_NtREL1B_Bsis_1/pae_INF2B_NtREL1B_Bsis_model_0.npz > color bfactor #1 palette alphafold 7655 atoms, 981 residues, atom bfactor range 27.4 to 98.3 > alphafold contacts /a toAtoms /b distance 4 Found 67 residue or atom pairs within distance 4 > close > open > /Users/obozkurt/Desktop/boltz_INF2B-NtREL1B-Bsis/INF2B-NtREL1B-Bsis_model_0.cif Summary of feedback from opening /Users/obozkurt/Desktop/boltz_INF2B-NtREL1B-Bsis/INF2B-NtREL1B-Bsis_model_0.cif --- warning | Atom C50 is not in the residue template for LIG /C:1 INF2B-NtREL1B-Bsis_model_0.cif title: . [more info...] Chain information for INF2B-NtREL1B-Bsis_model_0.cif #1 --- Chain | Description A | . B | . Non-standard residues in INF2B-NtREL1B-Bsis_model_0.cif #1 --- LIG — (LIG) No chain in structure corresponds to chain ID given in local score info (chain 'C') Computing secondary structure > ui tool show Contacts > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file > /Users/obozkurt/Desktop/boltz_INF2B-NtREL1B-Bsis/pae_INF2B-NtREL1B-Bsis_model_0.npz > color bfactor #1 palette alphafold 8030 atoms, 1038 residues, atom bfactor range 27.7 to 98 > alphafold contacts /a toAtoms /b distance 4 Found 150 residue or atom pairs within distance 4 > color bychain > select /A:1-169 1170 atoms, 1186 bonds, 169 residues, 1 model selected > color sel dim gray > select /A:1-169 1170 atoms, 1186 bonds, 169 residues, 1 model selected > color sel white > color sel dim gray > select /B:1-868 6832 atoms, 6967 bonds, 868 residues, 1 model selected > color sel white > select clear > select :LIG 28 atoms, 31 bonds, 1 residue, 1 model selected > color sel black > color sel cyan > select clear Alignment identifier is 1/A Alignment identifier is 1/B > select /A:39-40 12 atoms, 11 bonds, 2 residues, 1 model selected > select /A:39-46 57 atoms, 57 bonds, 8 residues, 1 model selected > select /A:85-86 15 atoms, 14 bonds, 2 residues, 1 model selected > select /A:85-99 105 atoms, 105 bonds, 15 residues, 1 model selected > select clear > movie record > roll y 2 180 [Repeated 1 time(s)] > select /A:169 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A 1170 atoms, 1186 bonds, 169 residues, 1 model selected > show sel surfaces > select clear > roll y 2 180 > movie encode output INF2B-NtREL1b-Bsis.mp4 Movie saved to INF2B-NtREL1b-Bsis.mp4 > close > open ""/Users/obozkurt/Downloads/CF4_AVR4_Chitin_Colab1 > (1)/predictions/CF4_AVR4_Chitin_Colab1/CF4_AVR4_Chitin_Colab1_model_0.cif"" Summary of feedback from opening /Users/obozkurt/Downloads/CF4_AVR4_Chitin_Colab1 (1)/predictions/CF4_AVR4_Chitin_Colab1/CF4_AVR4_Chitin_Colab1_model_0.cif --- warning | Atom C44 is not in the residue template for LIG /C:1 CF4_AVR4_Chitin_Colab1_model_0.cif title: . [more info...] Chain information for CF4_AVR4_Chitin_Colab1_model_0.cif #1 --- Chain | Description A | . B | . Non-standard residues in CF4_AVR4_Chitin_Colab1_model_0.cif #1 --- LIG — (LIG) No chain in structure corresponds to chain ID given in local score info (chain 'C') Computing secondary structure > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file ""/Users/obozkurt/Downloads/CF4_AVR4_Chitin_Colab1 > (1)/predictions/CF4_AVR4_Chitin_Colab1/plddt_CF4_AVR4_Chitin_Colab1_model_0.npz"" Traceback (most recent call last): File ""/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/alphafold/pae.py"", line 186, in _open_pae self._open_pae_from_file(s) File ""/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/alphafold/pae.py"", line 212, in _open_pae_from_file run(self.session, cmd) File ""/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3219, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/alphafold/pae.py"", line 1462, in alphafold_pae pae = AlphaFoldPAE(file, structure) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/alphafold/pae.py"", line 980, in __init__ self._pae_matrix = read_pae_matrix(pae_path) ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/alphafold/pae.py"", line 1226, in read_pae_matrix return read_numpy_pae_matrix(path) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/alphafold/pae.py"", line 1287, in read_numpy_pae_matrix pae = pae['pae'] ~~~^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/numpy/lib/npyio.py"", line 263, in __getitem__ raise KeyError(f""{key} is not a file in the archive"") KeyError: 'pae is not a file in the archive' KeyError: 'pae is not a file in the archive' File ""/Applications/ChimeraX-1.10-rc2025.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/numpy/lib/npyio.py"", line 263, in __getitem__ raise KeyError(f""{key} is not a file in the archive"") See log for complete Python traceback. OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 Max OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,10 Model Number: MRX53B/A Chip: Apple M3 Max Total Number of Cores: 14 (10 performance and 4 efficiency) Memory: 36 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 3 days, 2 hours, 31 minutes Graphics/Displays: Apple M3 Max: Chipset Model: Apple M3 Max Type: GPU Bus: Built-In Total Number of Cores: 30 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.4.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.3.4 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.18 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10rc202505300032 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.1 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.8.2 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.58.1 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.13.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.3.5 pytest-cov: 6.1.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 26.4.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.13.2 tzdata: 2025.2 urllib3: 2.4.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Structure Prediction fixed all ChimeraX